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39 collection of in-line ready operations:
41 lookup-table optimized scalar operations:
42 real gmx_invsqrt(real x)
43 void vecinvsqrt(real in[],real out[],int n)
44 void vecrecip(real in[],real out[],int n)
49 void rvec_add(const rvec a,const rvec b,rvec c) c = a + b
50 void dvec_add(const dvec a,const dvec b,dvec c) c = a + b
51 void ivec_add(const ivec a,const ivec b,ivec c) c = a + b
52 void rvec_inc(rvec a,const rvec b) a += b
53 void dvec_inc(dvec a,const dvec b) a += b
54 void ivec_inc(ivec a,const ivec b) a += b
55 void rvec_sub(const rvec a,const rvec b,rvec c) c = a - b
56 void dvec_sub(const dvec a,const dvec b,dvec c) c = a - b
57 void rvec_dec(rvec a,rvec b) a -= b
58 void copy_rvec(const rvec a,rvec b) b = a (reals)
59 void copy_dvec(const dvec a,dvec b) b = a (reals)
60 void copy_ivec(const ivec a,ivec b) b = a (integers)
61 void ivec_sub(const ivec a,const ivec b,ivec c) c = a - b
62 void svmul(real a,rvec v1,rvec v2) v2 = a * v1
63 void dsvmul(double a,dvec v1,dvec v2) v2 = a * v1
64 void clear_rvec(rvec a) a = 0
65 void clear_dvec(dvec a) a = 0
66 void clear_ivec(rvec a) a = 0
67 void clear_rvecs(int n,rvec v[])
68 real iprod(rvec a,rvec b) = a . b (inner product)
69 double diprod(dvec a,dvec b) = a . b (inner product)
70 real iiprod(ivec a,ivec b) = a . b (integers)
71 real norm2(rvec a) = | a |^2 ( = x*y*z )
72 double dnorm2(dvec a) = | a |^2 ( = x*y*z )
73 real norm(rvec a) = | a |
74 double dnorm(dvec a) = | a |
75 void cprod(rvec a,rvec b,rvec c) c = a x b (cross product)
76 void dprod(rvec a,rvec b,rvec c) c = a x b (cross product)
77 void dprod(rvec a,rvec b,rvec c) c = a * b (direct product)
78 real cos_angle(rvec a,rvec b)
79 real cos_angle_no_table(rvec a,rvec b)
80 real distance2(rvec v1, rvec v2) = | v2 - v1 |^2
81 void unitv(rvec src,rvec dest) dest = src / |src|
82 void unitv_no_table(rvec src,rvec dest) dest = src / |src|
84 matrix (3x3) operations:
85 ! indicates that dest should not be the same as a, b or src
86 the _ur0 varieties work on matrices that have only zeros
87 in the upper right part, such as box matrices, these varieties
88 could produce less rounding errors, not due to the operations themselves,
89 but because the compiler can easier recombine the operations
90 void copy_mat(matrix a,matrix b) b = a
91 void clear_mat(matrix a) a = 0
92 void mmul(matrix a,matrix b,matrix dest) ! dest = a . b
93 void mmul_ur0(matrix a,matrix b,matrix dest) dest = a . b
94 void transpose(matrix src,matrix dest) ! dest = src*
95 void tmmul(matrix a,matrix b,matrix dest) ! dest = a* . b
96 void mtmul(matrix a,matrix b,matrix dest) ! dest = a . b*
97 real det(matrix a) = det(a)
98 void m_add(matrix a,matrix b,matrix dest) dest = a + b
99 void m_sub(matrix a,matrix b,matrix dest) dest = a - b
100 void msmul(matrix m1,real r1,matrix dest) dest = r1 * m1
101 void m_inv_ur0(matrix src,matrix dest) dest = src^-1
102 void m_inv(matrix src,matrix dest) ! dest = src^-1
103 void mvmul(matrix a,rvec src,rvec dest) ! dest = a . src
104 void mvmul_ur0(matrix a,rvec src,rvec dest) dest = a . src
105 void tmvmul_ur0(matrix a,rvec src,rvec dest) dest = a* . src
106 real trace(matrix m) = trace(m)
109 #include "types/simple.h"
111 #include "typedefs.h"
112 #include "sysstuff.h"
113 #include "gmx_fatal.h"
119 } /* avoid screwing up indentation */
123 #define EXP_LSB 0x00800000
124 #define EXP_MASK 0x7f800000
126 #define FRACT_MASK 0x007fffff
127 #define FRACT_SIZE 11 /* significant part of fraction */
128 #define FRACT_SHIFT (EXP_SHIFT-FRACT_SIZE)
129 #define EXP_ADDR(val) (((val)&EXP_MASK)>>EXP_SHIFT)
130 #define FRACT_ADDR(val) (((val)&(FRACT_MASK|EXP_LSB))>>FRACT_SHIFT)
132 #define PR_VEC(a) a[XX],a[YY],a[ZZ]
134 #ifdef GMX_SOFTWARE_INVSQRT
135 extern const unsigned int * gmx_invsqrt_exptab;
136 extern const unsigned int * gmx_invsqrt_fracttab;
147 #ifdef GMX_SOFTWARE_INVSQRT
148 static real gmx_invsqrt(real x)
151 const real three=3.0;
152 t_convert result,bit_pattern;
153 unsigned int exp,fract;
161 exp = EXP_ADDR(bit_pattern.bval);
162 fract = FRACT_ADDR(bit_pattern.bval);
163 result.bval=gmx_invsqrt_exptab[exp] | gmx_invsqrt_fracttab[fract];
166 y=(half*lu*(three-((x*lu)*lu)));
168 y2=(half*y*(three-((x*y)*y)));
170 return y2; /* 10 Flops */
172 return y; /* 5 Flops */
176 #endif /* gmx_invsqrt */
178 #ifdef GMX_POWERPC_SQRT
179 static real gmx_invsqrt(real x)
182 const real three=3.0;
183 t_convert result,bit_pattern;
184 unsigned int exp,fract;
191 lu = __frsqrte((double)x);
193 y=(half*lu*(three-((x*lu)*lu)));
195 #if (GMX_POWERPC_SQRT==2)
196 /* Extra iteration required */
197 y=(half*y*(three-((x*y)*y)));
201 y2=(half*y*(three-((x*y)*y)));
203 return y2; /* 10 Flops */
205 return y; /* 5 Flops */
209 #endif /* powerpc_invsqrt */
213 #define gmx_invsqrt(x) (1.0f/sqrt(x))
220 static real sqr(real x)
225 static gmx_inline double dsqr(double x)
230 /* Maclaurin series for sinh(x)/x, useful for NH chains and MTTK pressure control
231 Here, we compute it to 10th order, which might be overkill, 8th is probably enough,
232 but it's not very much more expensive. */
234 static gmx_inline real series_sinhx(real x)
237 return (1 + (x2/6.0)*(1 + (x2/20.0)*(1 + (x2/42.0)*(1 + (x2/72.0)*(1 + (x2/110.0))))));
240 void vecinvsqrt(real in[],real out[],int n);
241 /* Perform out[i]=1.0/sqrt(in[i]) for n elements */
244 void vecrecip(real in[],real out[],int n);
245 /* Perform out[i]=1.0/(in[i]) for n elements */
247 /* Note: If you need a fast version of vecinvsqrt
248 * and/or vecrecip, call detectcpu() and run the SSE/3DNow/SSE2/Altivec
249 * versions if your hardware supports it.
251 * To use those routines, your memory HAS TO BE CACHE-ALIGNED.
252 * Use snew_aligned(ptr,size,32) to allocate and sfree_aligned to free.
256 static gmx_inline void rvec_add(const rvec a,const rvec b,rvec c)
269 static gmx_inline void dvec_add(const dvec a,const dvec b,dvec c)
282 static gmx_inline void ivec_add(const ivec a,const ivec b,ivec c)
295 static gmx_inline void rvec_inc(rvec a,const rvec b)
308 static gmx_inline void dvec_inc(dvec a,const dvec b)
321 static gmx_inline void rvec_sub(const rvec a,const rvec b,rvec c)
334 static gmx_inline void dvec_sub(const dvec a,const dvec b,dvec c)
347 static gmx_inline void rvec_dec(rvec a,const rvec b)
360 static gmx_inline void copy_rvec(const rvec a,rvec b)
367 static gmx_inline void copy_rvecn(rvec *a,rvec *b,int startn, int endn)
370 for (i=startn;i<endn;i++) {
377 static gmx_inline void copy_dvec(const dvec a,dvec b)
384 static gmx_inline void copy_ivec(const ivec a,ivec b)
391 static gmx_inline void ivec_sub(const ivec a,const ivec b,ivec c)
404 static gmx_inline void copy_mat(matrix a,matrix b)
406 copy_rvec(a[XX],b[XX]);
407 copy_rvec(a[YY],b[YY]);
408 copy_rvec(a[ZZ],b[ZZ]);
411 static gmx_inline void svmul(real a,const rvec v1,rvec v2)
418 static gmx_inline void dsvmul(double a,const dvec v1,dvec v2)
425 static gmx_inline real distance2(const rvec v1,const rvec v2)
427 return sqr(v2[XX]-v1[XX]) + sqr(v2[YY]-v1[YY]) + sqr(v2[ZZ]-v1[ZZ]);
430 static gmx_inline void clear_rvec(rvec a)
432 /* The ibm compiler has problems with inlining this
433 * when we use a const real variable
440 static gmx_inline void clear_dvec(dvec a)
442 /* The ibm compiler has problems with inlining this
443 * when we use a const real variable
450 static gmx_inline void clear_ivec(ivec a)
457 static gmx_inline void clear_rvecs(int n,rvec v[])
459 /* memset(v[0],0,DIM*n*sizeof(v[0][0])); */
466 static gmx_inline void clear_mat(matrix a)
468 /* memset(a[0],0,DIM*DIM*sizeof(a[0][0])); */
472 a[XX][XX]=a[XX][YY]=a[XX][ZZ]=nul;
473 a[YY][XX]=a[YY][YY]=a[YY][ZZ]=nul;
474 a[ZZ][XX]=a[ZZ][YY]=a[ZZ][ZZ]=nul;
477 static gmx_inline real iprod(const rvec a,const rvec b)
479 return (a[XX]*b[XX]+a[YY]*b[YY]+a[ZZ]*b[ZZ]);
482 static gmx_inline double diprod(const dvec a,const dvec b)
484 return (a[XX]*b[XX]+a[YY]*b[YY]+a[ZZ]*b[ZZ]);
487 static gmx_inline int iiprod(const ivec a,const ivec b)
489 return (a[XX]*b[XX]+a[YY]*b[YY]+a[ZZ]*b[ZZ]);
492 static gmx_inline real norm2(const rvec a)
494 return a[XX]*a[XX]+a[YY]*a[YY]+a[ZZ]*a[ZZ];
497 static gmx_inline double dnorm2(const dvec a)
499 return a[XX]*a[XX]+a[YY]*a[YY]+a[ZZ]*a[ZZ];
503 * As dnorm() uses sqrt() (which is slow) _only_ use it if you are sure you
504 * don't need 1/dnorm(), otherwise use dnorm2()*dinvnorm(). */
505 static gmx_inline double dnorm(const dvec a)
507 return sqrt(diprod(a, a));
511 * As norm() uses sqrtf() (which is slow) _only_ use it if you are sure you
512 * don't need 1/norm(), otherwise use norm2()*invnorm(). */
513 static gmx_inline real norm(const rvec a)
515 /* This is ugly, but we deliberately do not define gmx_sqrt() and handle the
516 * float/double case here instead to avoid gmx_sqrt() being accidentally used. */
520 return sqrtf(iprod(a, a));
524 static gmx_inline real invnorm(const rvec a)
526 return gmx_invsqrt(norm2(a));
529 static gmx_inline real dinvnorm(const dvec a)
531 return gmx_invsqrt(dnorm2(a));
535 * Do _not_ use these routines to calculate the angle between two vectors
536 * as acos(cos_angle(u,v)). While it might seem obvious, the acos function
537 * is very flat close to -1 and 1, which will lead to accuracy-loss.
538 * Instead, use the new gmx_angle() function directly.
540 static gmx_inline real
541 cos_angle(const rvec a,const rvec b)
544 * ax*bx + ay*by + az*bz
545 * cos-vec (a,b) = ---------------------
550 double aa,bb,ip,ipa,ipb,ipab; /* For accuracy these must be double! */
553 for(m=0; (m<DIM); m++) { /* 18 */
562 cosval = ip*gmx_invsqrt(ipab); /* 7 */
575 * Do _not_ use these routines to calculate the angle between two vectors
576 * as acos(cos_angle(u,v)). While it might seem obvious, the acos function
577 * is very flat close to -1 and 1, which will lead to accuracy-loss.
578 * Instead, use the new gmx_angle() function directly.
580 static gmx_inline real
581 cos_angle_no_table(const rvec a,const rvec b)
583 /* This version does not need the invsqrt lookup table */
586 double aa,bb,ip,ipa,ipb; /* For accuracy these must be double! */
589 for(m=0; (m<DIM); m++) { /* 18 */
596 cosval=ip/sqrt(ipa*ipb); /* 12 */
607 static gmx_inline void cprod(const rvec a,const rvec b,rvec c)
609 c[XX]=a[YY]*b[ZZ]-a[ZZ]*b[YY];
610 c[YY]=a[ZZ]*b[XX]-a[XX]*b[ZZ];
611 c[ZZ]=a[XX]*b[YY]-a[YY]*b[XX];
614 static gmx_inline void dcprod(const dvec a,const dvec b,dvec c)
616 c[XX]=a[YY]*b[ZZ]-a[ZZ]*b[YY];
617 c[YY]=a[ZZ]*b[XX]-a[XX]*b[ZZ];
618 c[ZZ]=a[XX]*b[YY]-a[YY]*b[XX];
621 /* This routine calculates the angle between a & b without any loss of accuracy close to 0/PI.
622 * If you only need cos(theta), use the cos_angle() routines to save a few cycles.
623 * This routine is faster than it might appear, since atan2 is accelerated on many CPUs (e.g. x86).
625 static gmx_inline real
626 gmx_angle(const rvec a, const rvec b)
636 return atan2(wlen,s);
639 static gmx_inline void mmul_ur0(matrix a,matrix b,matrix dest)
641 dest[XX][XX]=a[XX][XX]*b[XX][XX];
644 dest[YY][XX]=a[YY][XX]*b[XX][XX]+a[YY][YY]*b[YY][XX];
645 dest[YY][YY]= a[YY][YY]*b[YY][YY];
647 dest[ZZ][XX]=a[ZZ][XX]*b[XX][XX]+a[ZZ][YY]*b[YY][XX]+a[ZZ][ZZ]*b[ZZ][XX];
648 dest[ZZ][YY]= a[ZZ][YY]*b[YY][YY]+a[ZZ][ZZ]*b[ZZ][YY];
649 dest[ZZ][ZZ]= a[ZZ][ZZ]*b[ZZ][ZZ];
652 static gmx_inline void mmul(matrix a,matrix b,matrix dest)
654 dest[XX][XX]=a[XX][XX]*b[XX][XX]+a[XX][YY]*b[YY][XX]+a[XX][ZZ]*b[ZZ][XX];
655 dest[YY][XX]=a[YY][XX]*b[XX][XX]+a[YY][YY]*b[YY][XX]+a[YY][ZZ]*b[ZZ][XX];
656 dest[ZZ][XX]=a[ZZ][XX]*b[XX][XX]+a[ZZ][YY]*b[YY][XX]+a[ZZ][ZZ]*b[ZZ][XX];
657 dest[XX][YY]=a[XX][XX]*b[XX][YY]+a[XX][YY]*b[YY][YY]+a[XX][ZZ]*b[ZZ][YY];
658 dest[YY][YY]=a[YY][XX]*b[XX][YY]+a[YY][YY]*b[YY][YY]+a[YY][ZZ]*b[ZZ][YY];
659 dest[ZZ][YY]=a[ZZ][XX]*b[XX][YY]+a[ZZ][YY]*b[YY][YY]+a[ZZ][ZZ]*b[ZZ][YY];
660 dest[XX][ZZ]=a[XX][XX]*b[XX][ZZ]+a[XX][YY]*b[YY][ZZ]+a[XX][ZZ]*b[ZZ][ZZ];
661 dest[YY][ZZ]=a[YY][XX]*b[XX][ZZ]+a[YY][YY]*b[YY][ZZ]+a[YY][ZZ]*b[ZZ][ZZ];
662 dest[ZZ][ZZ]=a[ZZ][XX]*b[XX][ZZ]+a[ZZ][YY]*b[YY][ZZ]+a[ZZ][ZZ]*b[ZZ][ZZ];
665 static gmx_inline void transpose(matrix src,matrix dest)
667 dest[XX][XX]=src[XX][XX];
668 dest[YY][XX]=src[XX][YY];
669 dest[ZZ][XX]=src[XX][ZZ];
670 dest[XX][YY]=src[YY][XX];
671 dest[YY][YY]=src[YY][YY];
672 dest[ZZ][YY]=src[YY][ZZ];
673 dest[XX][ZZ]=src[ZZ][XX];
674 dest[YY][ZZ]=src[ZZ][YY];
675 dest[ZZ][ZZ]=src[ZZ][ZZ];
678 static gmx_inline void tmmul(matrix a,matrix b,matrix dest)
680 /* Computes dest=mmul(transpose(a),b,dest) - used in do_pr_pcoupl */
681 dest[XX][XX]=a[XX][XX]*b[XX][XX]+a[YY][XX]*b[YY][XX]+a[ZZ][XX]*b[ZZ][XX];
682 dest[XX][YY]=a[XX][XX]*b[XX][YY]+a[YY][XX]*b[YY][YY]+a[ZZ][XX]*b[ZZ][YY];
683 dest[XX][ZZ]=a[XX][XX]*b[XX][ZZ]+a[YY][XX]*b[YY][ZZ]+a[ZZ][XX]*b[ZZ][ZZ];
684 dest[YY][XX]=a[XX][YY]*b[XX][XX]+a[YY][YY]*b[YY][XX]+a[ZZ][YY]*b[ZZ][XX];
685 dest[YY][YY]=a[XX][YY]*b[XX][YY]+a[YY][YY]*b[YY][YY]+a[ZZ][YY]*b[ZZ][YY];
686 dest[YY][ZZ]=a[XX][YY]*b[XX][ZZ]+a[YY][YY]*b[YY][ZZ]+a[ZZ][YY]*b[ZZ][ZZ];
687 dest[ZZ][XX]=a[XX][ZZ]*b[XX][XX]+a[YY][ZZ]*b[YY][XX]+a[ZZ][ZZ]*b[ZZ][XX];
688 dest[ZZ][YY]=a[XX][ZZ]*b[XX][YY]+a[YY][ZZ]*b[YY][YY]+a[ZZ][ZZ]*b[ZZ][YY];
689 dest[ZZ][ZZ]=a[XX][ZZ]*b[XX][ZZ]+a[YY][ZZ]*b[YY][ZZ]+a[ZZ][ZZ]*b[ZZ][ZZ];
692 static gmx_inline void mtmul(matrix a,matrix b,matrix dest)
694 /* Computes dest=mmul(a,transpose(b),dest) - used in do_pr_pcoupl */
695 dest[XX][XX]=a[XX][XX]*b[XX][XX]+a[XX][YY]*b[XX][YY]+a[XX][ZZ]*b[XX][ZZ];
696 dest[XX][YY]=a[XX][XX]*b[YY][XX]+a[XX][YY]*b[YY][YY]+a[XX][ZZ]*b[YY][ZZ];
697 dest[XX][ZZ]=a[XX][XX]*b[ZZ][XX]+a[XX][YY]*b[ZZ][YY]+a[XX][ZZ]*b[ZZ][ZZ];
698 dest[YY][XX]=a[YY][XX]*b[XX][XX]+a[YY][YY]*b[XX][YY]+a[YY][ZZ]*b[XX][ZZ];
699 dest[YY][YY]=a[YY][XX]*b[YY][XX]+a[YY][YY]*b[YY][YY]+a[YY][ZZ]*b[YY][ZZ];
700 dest[YY][ZZ]=a[YY][XX]*b[ZZ][XX]+a[YY][YY]*b[ZZ][YY]+a[YY][ZZ]*b[ZZ][ZZ];
701 dest[ZZ][XX]=a[ZZ][XX]*b[XX][XX]+a[ZZ][YY]*b[XX][YY]+a[ZZ][ZZ]*b[XX][ZZ];
702 dest[ZZ][YY]=a[ZZ][XX]*b[YY][XX]+a[ZZ][YY]*b[YY][YY]+a[ZZ][ZZ]*b[YY][ZZ];
703 dest[ZZ][ZZ]=a[ZZ][XX]*b[ZZ][XX]+a[ZZ][YY]*b[ZZ][YY]+a[ZZ][ZZ]*b[ZZ][ZZ];
706 static gmx_inline real det(matrix a)
708 return ( a[XX][XX]*(a[YY][YY]*a[ZZ][ZZ]-a[ZZ][YY]*a[YY][ZZ])
709 -a[YY][XX]*(a[XX][YY]*a[ZZ][ZZ]-a[ZZ][YY]*a[XX][ZZ])
710 +a[ZZ][XX]*(a[XX][YY]*a[YY][ZZ]-a[YY][YY]*a[XX][ZZ]));
713 static gmx_inline void m_add(matrix a,matrix b,matrix dest)
715 dest[XX][XX]=a[XX][XX]+b[XX][XX];
716 dest[XX][YY]=a[XX][YY]+b[XX][YY];
717 dest[XX][ZZ]=a[XX][ZZ]+b[XX][ZZ];
718 dest[YY][XX]=a[YY][XX]+b[YY][XX];
719 dest[YY][YY]=a[YY][YY]+b[YY][YY];
720 dest[YY][ZZ]=a[YY][ZZ]+b[YY][ZZ];
721 dest[ZZ][XX]=a[ZZ][XX]+b[ZZ][XX];
722 dest[ZZ][YY]=a[ZZ][YY]+b[ZZ][YY];
723 dest[ZZ][ZZ]=a[ZZ][ZZ]+b[ZZ][ZZ];
726 static gmx_inline void m_sub(matrix a,matrix b,matrix dest)
728 dest[XX][XX]=a[XX][XX]-b[XX][XX];
729 dest[XX][YY]=a[XX][YY]-b[XX][YY];
730 dest[XX][ZZ]=a[XX][ZZ]-b[XX][ZZ];
731 dest[YY][XX]=a[YY][XX]-b[YY][XX];
732 dest[YY][YY]=a[YY][YY]-b[YY][YY];
733 dest[YY][ZZ]=a[YY][ZZ]-b[YY][ZZ];
734 dest[ZZ][XX]=a[ZZ][XX]-b[ZZ][XX];
735 dest[ZZ][YY]=a[ZZ][YY]-b[ZZ][YY];
736 dest[ZZ][ZZ]=a[ZZ][ZZ]-b[ZZ][ZZ];
739 static gmx_inline void msmul(matrix m1,real r1,matrix dest)
741 dest[XX][XX]=r1*m1[XX][XX];
742 dest[XX][YY]=r1*m1[XX][YY];
743 dest[XX][ZZ]=r1*m1[XX][ZZ];
744 dest[YY][XX]=r1*m1[YY][XX];
745 dest[YY][YY]=r1*m1[YY][YY];
746 dest[YY][ZZ]=r1*m1[YY][ZZ];
747 dest[ZZ][XX]=r1*m1[ZZ][XX];
748 dest[ZZ][YY]=r1*m1[ZZ][YY];
749 dest[ZZ][ZZ]=r1*m1[ZZ][ZZ];
752 static gmx_inline void m_inv_ur0(matrix src,matrix dest)
754 double tmp = src[XX][XX]*src[YY][YY]*src[ZZ][ZZ];
755 if (fabs(tmp) <= 100*GMX_REAL_MIN)
756 gmx_fatal(FARGS,"Can not invert matrix, determinant is zero");
758 dest[XX][XX] = 1/src[XX][XX];
759 dest[YY][YY] = 1/src[YY][YY];
760 dest[ZZ][ZZ] = 1/src[ZZ][ZZ];
761 dest[ZZ][XX] = (src[YY][XX]*src[ZZ][YY]*dest[YY][YY]
762 - src[ZZ][XX])*dest[XX][XX]*dest[ZZ][ZZ];
763 dest[YY][XX] = -src[YY][XX]*dest[XX][XX]*dest[YY][YY];
764 dest[ZZ][YY] = -src[ZZ][YY]*dest[YY][YY]*dest[ZZ][ZZ];
770 static gmx_inline void m_inv(matrix src,matrix dest)
772 const real smallreal = (real)1.0e-24;
773 const real largereal = (real)1.0e24;
780 if ((fc <= smallreal) || (fc >= largereal))
781 gmx_fatal(FARGS,"Can not invert matrix, determinant = %e",deter);
783 dest[XX][XX]= c*(src[YY][YY]*src[ZZ][ZZ]-src[ZZ][YY]*src[YY][ZZ]);
784 dest[XX][YY]=-c*(src[XX][YY]*src[ZZ][ZZ]-src[ZZ][YY]*src[XX][ZZ]);
785 dest[XX][ZZ]= c*(src[XX][YY]*src[YY][ZZ]-src[YY][YY]*src[XX][ZZ]);
786 dest[YY][XX]=-c*(src[YY][XX]*src[ZZ][ZZ]-src[ZZ][XX]*src[YY][ZZ]);
787 dest[YY][YY]= c*(src[XX][XX]*src[ZZ][ZZ]-src[ZZ][XX]*src[XX][ZZ]);
788 dest[YY][ZZ]=-c*(src[XX][XX]*src[YY][ZZ]-src[YY][XX]*src[XX][ZZ]);
789 dest[ZZ][XX]= c*(src[YY][XX]*src[ZZ][YY]-src[ZZ][XX]*src[YY][YY]);
790 dest[ZZ][YY]=-c*(src[XX][XX]*src[ZZ][YY]-src[ZZ][XX]*src[XX][YY]);
791 dest[ZZ][ZZ]= c*(src[XX][XX]*src[YY][YY]-src[YY][XX]*src[XX][YY]);
794 static gmx_inline void mvmul(matrix a,const rvec src,rvec dest)
796 dest[XX]=a[XX][XX]*src[XX]+a[XX][YY]*src[YY]+a[XX][ZZ]*src[ZZ];
797 dest[YY]=a[YY][XX]*src[XX]+a[YY][YY]*src[YY]+a[YY][ZZ]*src[ZZ];
798 dest[ZZ]=a[ZZ][XX]*src[XX]+a[ZZ][YY]*src[YY]+a[ZZ][ZZ]*src[ZZ];
801 static gmx_inline void mvmul_ur0(matrix a,const rvec src,rvec dest)
803 dest[ZZ]=a[ZZ][XX]*src[XX]+a[ZZ][YY]*src[YY]+a[ZZ][ZZ]*src[ZZ];
804 dest[YY]=a[YY][XX]*src[XX]+a[YY][YY]*src[YY];
805 dest[XX]=a[XX][XX]*src[XX];
808 static gmx_inline void tmvmul_ur0(matrix a,const rvec src,rvec dest)
810 dest[XX]=a[XX][XX]*src[XX]+a[YY][XX]*src[YY]+a[ZZ][XX]*src[ZZ];
811 dest[YY]= a[YY][YY]*src[YY]+a[ZZ][YY]*src[ZZ];
812 dest[ZZ]= a[ZZ][ZZ]*src[ZZ];
815 static gmx_inline void unitv(const rvec src,rvec dest)
819 linv=gmx_invsqrt(norm2(src));
820 dest[XX]=linv*src[XX];
821 dest[YY]=linv*src[YY];
822 dest[ZZ]=linv*src[ZZ];
825 static gmx_inline void unitv_no_table(const rvec src,rvec dest)
829 linv=1.0/sqrt(norm2(src));
830 dest[XX]=linv*src[XX];
831 dest[YY]=linv*src[YY];
832 dest[ZZ]=linv*src[ZZ];
835 static void calc_lll(rvec box,rvec lll)
837 lll[XX] = 2.0*M_PI/box[XX];
838 lll[YY] = 2.0*M_PI/box[YY];
839 lll[ZZ] = 2.0*M_PI/box[ZZ];
842 static gmx_inline real trace(matrix m)
844 return (m[XX][XX]+m[YY][YY]+m[ZZ][ZZ]);
847 static gmx_inline real _divide_err(real a,real b,const char *file,int line)
849 if (fabs(b) <= GMX_REAL_MIN)
850 gmx_fatal(FARGS,"Dividing by zero, file %s, line %d",file,line);
854 static gmx_inline int _mod(int a,int b,char *file,int line)
857 gmx_fatal(FARGS,"Modulo zero, file %s, line %d",file,line);
861 /* Operations on multidimensional rvecs, used e.g. in edsam.c */
862 static void m_rveccopy(int dim, rvec *a, rvec *b)
867 for (i=0; i<dim; i++)
868 copy_rvec(a[i],b[i]);
871 /*computer matrix vectors from base vectors and angles */
872 static void matrix_convert(matrix box, rvec vec, rvec angle)
874 svmul(DEG2RAD,angle,angle);
875 box[XX][XX] = vec[XX];
876 box[YY][XX] = vec[YY]*cos(angle[ZZ]);
877 box[YY][YY] = vec[YY]*sin(angle[ZZ]);
878 box[ZZ][XX] = vec[ZZ]*cos(angle[YY]);
879 box[ZZ][YY] = vec[ZZ]
880 *(cos(angle[XX])-cos(angle[YY])*cos(angle[ZZ]))/sin(angle[ZZ]);
881 box[ZZ][ZZ] = sqrt(sqr(vec[ZZ])
882 -box[ZZ][XX]*box[ZZ][XX]-box[ZZ][YY]*box[ZZ][YY]);
885 #define divide_err(a,b) _divide_err((a),(b),__FILE__,__LINE__)
886 #define mod(a,b) _mod((a),(b),__FILE__,__LINE__)